Long considered[who?] a failure, his reputation has been reevaluated by recent historiography[who?] which has shown that, in a period of difficulty, he was a capable administrator of an immense department which had responsibility for the French Navy, trade, colonies, matters of religion, Paris, the royal household and for finances. He conducted a census of the population from 1693 onwards, the first since Vauban's of 1678. At court he was an opponent of Fénelon and the Quietists.

In 1668 he married Marie de Maupeou. They had one son, Jérôme Phélypeaux (1674–1747), comte de Pontchartrain.

He resigned in 1714 for having failed to affix the seals to the decree of 5 July 1714, condemning a document by the Bishop of Metz, Henri-Charles de Coislin, as contrary to the papal bullUnigenitus. He had found it difficult to reconcile his religious beliefs with those of the increasingly authoritarian Louis XIV. He retired to an Oratorian institution where he died in 1727.

In addition, Île Philippaux and Isle Pontchartrain which appear on early maps of Lake Superior are believed to have been named after him. Neither island, it was later determined, actually existed. They are thought to have been added to maps by French explorers hoping that Phélypeaux would be inspired to provide more funds to explore the area.[1]